centWave Parameters
ppm, peakwidth, snthresh, prefilter, mzCenterFun, integrate, mzdiff, fitgauss, scanrange, noise.
All centWave parameters require fine-tuning for each assay type and mass analyser.
The following illustrates all xcms parameters.
Explanation of parameters:
| Parameter | Explanation | Pre-adjusted value |
|---|---|---|
| ppm | signal deviation in m/z dimension | 25 |
| peakwidht | range peak elution times in seconds | 20-50 s |
| snthresh | signals below this locally defined value are not considered as signals | 10 |
| prefilter | Peak definition: how many data points (n) should be above a certain intensity threshold (I) | k=3, I=100 |
| mzdiff | Closeness of two signals in mz dimension | -0.001 |
| noise | Intensity threshold, values below are considered instrument noise | 0 |
| integrate | Integration method: 1 - Mexican hat filtered data (less exact), 2- real data (prone to noise) | 1 |
| mzCenterFun | Function to calculate m/z center of chromatographic peak | weighted Mean (wMean) |
| fitgauss | Peak fitting using Gauss distribution | FALSE |
ppm
mzdiff
noise
snthresh
peakwidth
prefilter
